11,000 years later, Rose is still carrying out the gruesome task so as to save the world. She meets Dart and decides to accompany the group not just because she's curious about the Red-Eye Dragoon Spirit, but because the determination of their group reminds her of the way she and her comrades used to be. As the journey goes on, more and more people are attracted by Dart and choose to follow him, and one after another, they are chosen by the remaining Dragoon Spirits.
As if the call of the new Dragoons, the re-emergence of Dragons and one antagonist's plot to steal all of the Divine Moon Objects weren't enough, more unexplained phenomena happen around the group: Shana is capable of hearing the Virages' voices that call her to them, and her presence wakes these ancient weapons of destruction from their long slumber. A ghost appears at the Temple of Shirley and it seems to know Rose and what her "sad journey" entails, though neither Dart nor Lavitz think about it too deeply. Dart's thoughts keep returning to the Black Monster, his search for it a journey parallel to the current mission.
And then, at the end of disc 2, the group crosses a Phantom Ship while at sea.
"(Th... this ship is...)" Rose recognizes the ship right away, but keeps it to herself, just as she has kept her secrets to herself. As the group decides to have a closer look at the ship, ghosts of the its former crew appear in front of them, frantically begging for help because they don't want to die. When they run into the ghost of the ship's captain, he reveals that everyone on the ship – the crew, the nanny, the knights and the newborn princess – was killed by the Black Monster. He asks the party to "destroy the fear" and send the souls of the knights to rest, as the ghosts' overwhelming regret over not having been able to protect the princess is what roots them to this world. As a fellow victim of the Black Monster, Dart in particular shows his disgust: "He killed people for no reason!" All the while, Rose remains silent.
This changes when Ghost Knights appear, still believing that they're fighting to protect Princess Louvia. If the player has read the hints at Rose's identity up to this point and correctly interpreted them, they might notice that the ghosts only attack Rose repeatedly at this point – the party, however, doesn't. They fight the ghosts under the assumption that the ghosts are misunderstanding, and that they are indiscriminately attacking any intruders. When the group passes judgement on the Black Monster's wrongdoings, Rose loses control in front of them for the very first time:
Albert: We are witnessing a tragedy from the past.
Shana: It's awful. Why did it have to do this?
Dart: The Black Monster!! How much does he have to kill before he satisfies himself!?
Rose: Stop it!! Sorry. What was I thinking? Let's move on. You want to know, don't you?
Her companions don't recognize the significance in that outburst, though the player might. More worrying is Shana, who finds herself at the center of attention again after she has been mysteriously called to the ship. The Ghost Knights protect her from creatures that have taken over the ship, address her as Princess Louvia, and fade away when she steps forward to tell that there is no Black Monster and that they needn't suffer any more. Finally, when they reach the deepest room on the ship and see a baby crib, they meet the last remaining soul – the ghost of a nanny.
Ghost Nanny: Princess Louvia, she was still young. If she wasn't a princess of Mille Seseau, this wouldn't have happened.
Shana: Princess of Mille Seseau?
Ghost Nanny: Oh my, you are...? Alive... Oh lord. It was not in vain. I have been wandering for 18 years and longing for you. I can now end everything. I can go to the place everyone is.
The ghost disappears, leaving Shana confused about her relationship to the ship's former passengers and the mysterious Princess Louvia. But for once, Rose has no input to give.
The Burden of Knowledge
After the adventure that has raised many more questions and established a possible link between Rose and Shana, Rose and Dart fall off the ship. Alone in a cave with an unconscious Dart, Rose reminisces about the Dragon Campaign and Zieg, the love she lost to Melbu Frahma's petrification spell and whom Dart resembles. The journey goes on once Dart and Rose meet up with the rest of the group, and when Rose splits from it for a while to visit Neet, Dart's hometown and the site of the last known tragedy brought forth by the Black Monster, the player learns that Rose assaulted the village 18 years ago in search of Princess Louvia. A dying woman's last words were what led her to pursue the Phantom Ship.
The past slowly but surely catches up to Rose over the course of disc 3 as the group is confronted with the mighty Divine Dragon and visits ruins of the past while calling upon Rose's knowledge. Rose knows of the Winglies' ancient tools that can harm even Dragons and Dragoons, sees through Meru, who meant to keep her Wingly identity secret, and shares long-lost knowledge with the group about ancient battle sites, all of which she delivers with a casual "I heard about it." while waving it off.
The name of Emperor Diaz, deceased leader of the Humans during the war against the Winglies, comes up several times during the quest, and Lloyd, the mysterious figure the party has been chasing, reveals that he's been working toward the utopia that he and Emperor Diaz desire. When he shares the version of the Moon Child myth he has been told by Emperor Diaz with the group, Rose interrupts him:
Lloyd: The "Moon Child" of this legend is the last species. It is the god that gives holy bliss to the world.
Rose: That's not true.
Lloyd: It is the truth. Then why does the Black Monster continue to kill the Moon Child?
Disc 3: Snowfield
Rose doesn't voice her objection to defend herself, but because Lloyd has become a person to be trusted at this point, so the consequences of misinformation may be disastrous – after all, they are now on a mission to take back Shana, who has been taken hostage in exchange for the Divine Moon Objects they have seized. Yet, Rose leaves it at that because she can't tell the party about her past and the burden she alone has to carry, for it would mean revealing that she's the Black Monster.
Nothing but the Truth
In the company of Lloyd, the group heads to Capital Vellweb, seat of the former Human emperor, to learn the truth: Shana's role in all of this, the significance of the Divine Moon Objects, the existence of Winglies, Virages, Dragons and Dragoons, the Black Monster, the Moon That Never Sets, the person who claims to be Diaz, the promise of a utopia – all the elements of the distant past are coming together.
At the throne of the emperor, Lloyd realizes he has been used by a false promise all along: rather than a utopia, what is brought forth by the Moon Child is total destruction. "Diaz" disposes of Lloyd and reveals his true identity to the party, a revelation that shocks both Dart and Rose to the core, for the man in front of them is none other than Dart's father and Rose's past love, previous holder of the Red-Eye Dragoon Spirit and hero of the Dragon Campaign: Zieg.
Believed by different parties to have died, once as a comrade to petrification, once as a father during the assault of Neet, Zieg now explains what has transpired since the victory over Melbu Frahma:
I have waited for 11,000 years. Time, almost eternal, dissolved the spell of Melbu. And I was released from captivity. Days spent with Rose became the eternal past. And I lived as the father of Dart in this age. Until the tragic day in Neet.
He thus reveals that Rose, too, is a hero from the past, and tells them of the accidental destruction of the Crystal Sphere, which used to hold the container of the soul of the God of Destruction, a role then assumed by the Moon Child – and with that, he exposes the identity of the one person responsible for deterring its birth: Rose, the Black Monster.
As if all of that weren't shocking enough already, he grabs Shana and informs Rose that Princess Louvia, who she killed 18 years ago in the belief that she was this cycle's Moon Child, had a twin sister – the actual Moon Child. That sister is Shana, the soul of the Virage Embryo and God of Destruction. In an instant, Dart cries out to demand Shana's release, and without hesitation, Rose rushes forward – to demand her death. But Rose's sword is repelled by Zieg's magic, he escapes with the unconscious Shana, and disc 3 ends.